Invasion by alien species is a worldwide conservation problem, posing the second largest threat to biodiversity. Invasive alien plants (IAP) have a range of negative impacts: transforming ecosystems, reducing biodiversity and compromising on the delivery of ecosystem functions and services. Management interventions, such as restoration, could alleviate some of these negative impacts. Passive restoration consists of the clearance of IAP but is often not sufficient for ecosystem recovery, hence the need for a more pro-active approach of active restoration, e.g. re-introduction of native species, in some instances. As restoration is a resource intensive budget-limited process; one needs to distinguish between areas needing passive or active management, and also prioritize areas to ensure efficiency and effectiveness. The fynbos biome in South Africa is one of the most invaded biomes in the country, and for which there has not yet been any regional prioritization of areas for restoration after IAP clearance. The aim of this study is two-fold, firstly to develop and illustrate a framework to distinguish between areas in need of active and passive restoration in the City of Cape Town and secondly, to prioritize restoration areas. A multi-scale approach will be used to identify and prioritize areas for restoration. At a large city scale, the ecosystem threshold concept will be applied, using ecological information and GIS. At a smaller catchment scale a novel ecosystem approach will be developed combining field sampling along with GIS. This study will be of particular value to land managers, conservationists and city planners.